Summary :Toxoplasma gondii has been described as a parasite with a low genetic diversity and a clonal population structure. The three main clonal lineages designated as type I, II or III largely predominate in Europe and North America. But strains not related to these main lineages circulate, notably, in other continents. They possess a shuffled combination of alleles that typify the three clonal types and unique polymorphisms detected by multilocus analysis. The population structure of Toxoplasma in these continents is also characterized by a higher genetic diversity associated with a lower linkage desequilibrium suggesting a role for genetic exchange. Due to their genomic diversity, it is difficult to draw global conclusions about their virulence. However, most of them are virulent in mice at isolation. Several reports also suggest a higher pathogenicity in humans and an association with ocular toxoplasmosis or severe cases of acquired toxoplasmosis in immunocompetent patients. T he three main types respond to the criteria for a clonal population structure of Toxoplasma (isolation of identical multilocus genotypes over large geographic areas and at interval of several years, and a strong linkage disequilibrium) (Tibayrenc et al., 1991). This simple clonal structure is accompanied by a low genetic divergence between the three main lineages (only ≈ 2 % divergence at the DNA sequence level between lineages). A large majority (84 %) of the of the single nucleotide polymorphisms (SNPs) identified among the three types are type I and II SNPs, type III polymorphisms (only 16 %) being located mainly on chromosome IV (Boyle et al., 2006). The assymetrical distribution of SNPs on chromosomes indicates that types I and III are second and first generation offspring, respectively, of a cross between a type II strain and one of two ancestral strains. The limited genetic diversity within each of these lineages and the low divergence between lineages strongly suggest that these three clonal lineages have expanded as the dominant strains relatively recently, from a common ancestor 10,000 years ago (Su et al., 2003).